The U.S. Department of Justice dismissed 89 percent of cases filed by FBI whistleblowers who said they had been retaliated against for exposing wrongdoing.

"Whistleblowers play an important role in safeguarding the federal government against waste, fraud and abuse, but they often risk retaliation from their employers as a result of their actions," the GAO report said.

The GAO examined the 62 complaints filed between 2009 and 2013, and found that 55 were rejected. The DOJ sided with the employees and awarded corrective action in only three cases.

The FBI occasionally took up to 10 years to handle the whistleblower retaliation complaints, and about a third of the complaints were simply tossed in the trash because the initial disclosure of wrongdoing wasn't filed with one of the nine high-level officials designated to handle complaints.

"For example," the report says, "in 2002, a former FBI agent alleged she suffered retaliation after disclosing that colleagues had stolen items from Ground Zero following the September 11, 2001, terrorist attacks. DOJ found in her favor over 10 years after she reported the retaliation."

According to Sen. Charles Grassley, R-Iowa, who commissioned the report, the FBI is the only federal agency that doesn't protect employees who complain to their immediate supervisors or follow the chain of command to make complaints.

"The FBI and Department of Justice, in particular, have a vested interest in investigating wrongdoing, yet when an FBI employee uncovers misconduct within the agency's own ranks, it's not so easy to sound the alarm without the risk of retaliation," Grassley said in a statement. "This report confirms that reforms are needed to empower whistle-blowers at FBI and ensure they are effectively and efficiently protected against retaliation in the workplace."

The report noted that by dismissing complaints that were potentially legitimate simply because they had not been properly filed, the Justice Department "could deny some whistleblowers access to recourse, permit retaliatory activity to go uninvestigated, and create a chilling effect for future whistleblowers."

Justice Department officials have promised to address some of the problems by "adding several more senior officials in FBI field offices to the list of individuals who may report protected disclosures," the GAO said, adding that there is no established time frame for the plan and the outcome is uncertain.